Most people know that sexual
reproduction creates offspring that are genetically distinct from
both of the their parents. That's true, but the genetic scrambling
that occurs is more significant than is sometimes reported. Let's
start by looking at chromosomes.

Like every other animal (or plant or pretty much any other organism),
your genetic endowment is carried in chunks of DNA called
chromosomes. You have 23 of these chunks, which are rather like
volumes in a set of encyclopedias. More completely, you have 23 pairs
of these volumes; one set was contributed by your mother and the
other by your father. Each of your parents had a complete set, also
consisting of a set from Mom and a set from Dad. When your mother
made the egg that became the zygote that became you, she provided you
with one copy of each volume in the set, and she chose those copies
randomly. For example, she may have chosen her dad's copy of
chromosome 1, but her mom's copy of chromosome 2. Just by virtue of
this random picking process, she made an egg with a shuffled version
of her own genetic cards. Dad did the same when he made his sperm,
and so your genetic complement is an amalgamation of your parents'
genomes which were amalgamations of your grandparents' genomes, and
so on.
But before the random picking process
occurred in the steps leading up to the final egg/sperm, something
remarkable happened to further shuffle the genetic deck. For each
chromosome, the different copies lined up with each other and
exchanged contents. In other words, a new chromosome 1 was made that
was an amalgamation of the maternal chromosome 1 and the paternal
chromosome 1. The two new versions were chromosomes unlike any in
your mom or dad; they were new creations, clearly designed to
maximize the diversity in your genetic inheritance. This process,
which is illustrated in the diagram below, is called crossing over.

The figure shows two instances of
crossing over, creating the amalgamations that are part white, part
black. In the real process, crossing over can occur at multiple sites
along the chromosome, so that the resulting amalgamations are
black-white-black-white and so on.

What this means is that you received,
from each of your parents, a set of chromosomes that included at
least some which were shuffled versions of their own chromosomes. And
more importantly, this means that the units of genetic material that
you received were much bigger than individual genes (which can barely
be visibly represented on a diagram like the one above) but typically
smaller than an entire chromosome. It's as if you were given a set of
encyclopedias in which individual volumes had chapters from one
version of that volume and chapters from another. Individual genes
would be merely pages. The basic lesson here is that you received
your genes from your parents in chunks, like chapters, and not one by
one, like pages.

What does this have to do with
hitchhiking? Well, suppose that in one of those chapters, meaning in
one section of one chromosome, there appeared a beneficial mutation
of some kind, and suppose that this mutation conferred an advantage
on every individual who carried it. Over a relatively short time
(evolutionarily speaking), that chapter could become a lot more
common in the population. It may even become so common that it's the
norm, in which case it would be considered to be fixed in the
population. (The process is then called fixation.) Notice,
importantly, that we said the chapter will become fixed. Why
not just the gene? Because the pieces of DNA that are passed down in
each generation are a lot bigger than that, as we just saw.

The basic message, then, is this: when
an organism inherits some new and beneficial gene, it inherits
everything in the vicinity of that gene as well. If that new and
beneficial gene becomes fixed in the population, then everything in
the vicinity will be fixed as well. The result is that when a strong
selection process acts, and drives a new gene to fixation in a
relatively short time, it leaves a mark on the genome: one chapter in
the set of encyclopedias will be oddly the same in everyone. That
chapter will display a lot less genetic diversity than other
chapters. That's the signature of recent positive selection,
resulting from a so-called selective sweep. And it results in
the fixation of a lot of stuff, most of which is just along for the
ride by virtue of being located in the same chapter as the beneficial
gene. All that other stuff got there by hitchhiking.

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Most people know that sexual
reproduction creates offspring that are genetically distinct from
both of the their parents. That's true, but the genetic scrambling
that occurs is more significant than is sometimes reported. Let's
start by looking at chromosomes.

Like every other animal (or plant or pretty much any other organism),
your genetic endowment is carried in chunks of DNA called
chromosomes. You have 23 of these chunks, which are rather like
volumes in a set of encyclopedias. More completely, you have 23 pairs
of these volumes; one set was contributed by your mother and the
other by your father. Each of your parents had a complete set, also
consisting of a set from Mom and a set from Dad. When your mother
made the egg that became the zygote that became you, she provided you
with one copy of each volume in the set, and she chose those copies
randomly. For example, she may have chosen her dad's copy of
chromosome 1, but her mom's copy of chromosome 2. Just by virtue of
this random picking process, she made an egg with a shuffled version
of her own genetic cards. Dad did the same when he made his sperm,
and so your genetic complement is an amalgamation of your parents'
genomes which were amalgamations of your grandparents' genomes, and
so on.
But before the random picking process
occurred in the steps leading up to the final egg/sperm, something
remarkable happened to further shuffle the genetic deck. For each
chromosome, the different copies lined up with each other and
exchanged contents. In other words, a new chromosome 1 was made that
was an amalgamation of the maternal chromosome 1 and the paternal
chromosome 1. The two new versions were chromosomes unlike any in
your mom or dad; they were new creations, clearly designed to
maximize the diversity in your genetic inheritance. This process,
which is illustrated in the diagram below, is called crossing over.

The figure shows two instances of
crossing over, creating the amalgamations that are part white, part
black. In the real process, crossing over can occur at multiple sites
along the chromosome, so that the resulting amalgamations are
black-white-black-white and so on.

What this means is that you received,
from each of your parents, a set of chromosomes that included at
least some which were shuffled versions of their own chromosomes. And
more importantly, this means that the units of genetic material that
you received were much bigger than individual genes (which can barely
be visibly represented on a diagram like the one above) but typically
smaller than an entire chromosome. It's as if you were given a set of
encyclopedias in which individual volumes had chapters from one
version of that volume and chapters from another. Individual genes
would be merely pages. The basic lesson here is that you received
your genes from your parents in chunks, like chapters, and not one by
one, like pages.

What does this have to do with
hitchhiking? Well, suppose that in one of those chapters, meaning in
one section of one chromosome, there appeared a beneficial mutation
of some kind, and suppose that this mutation conferred an advantage
on every individual who carried it. Over a relatively short time
(evolutionarily speaking), that chapter could become a lot more
common in the population. It may even become so common that it's the
norm, in which case it would be considered to be fixed in the
population. (The process is then called fixation.) Notice,
importantly, that we said the chapter will become fixed. Why
not just the gene? Because the pieces of DNA that are passed down in
each generation are a lot bigger than that, as we just saw.

The basic message, then, is this: when
an organism inherits some new and beneficial gene, it inherits
everything in the vicinity of that gene as well. If that new and
beneficial gene becomes fixed in the population, then everything in
the vicinity will be fixed as well. The result is that when a strong
selection process acts, and drives a new gene to fixation in a
relatively short time, it leaves a mark on the genome: one chapter in
the set of encyclopedias will be oddly the same in everyone. That
chapter will display a lot less genetic diversity than other
chapters. That's the signature of recent positive selection,
resulting from a so-called selective sweep. And it results in
the fixation of a lot of stuff, most of which is just along for the
ride by virtue of being located in the same chapter as the beneficial
gene. All that other stuff got there by hitchhiking.